Strain identifier

BacDive ID: 14138

Type strain: Yes

Species: Olivibacter domesticus

Strain Designation: DC-186

Strain history: CIP <- 2007, CCUG

NCBI tax ID(s): 1123028 (strain), 407022 (species)

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General

@ref: 7678

BacDive-ID: 14138

DSM-Number: 18733

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Olivibacter domesticus DC-186 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from home-made compost.

NCBI tax id

NCBI tax idMatching level
1123028strain
407022species

strain history

@refhistory
7678<- C. M. Manaia, Escola Superior de Biotecnol., Univ. Catolica Portuguesa, Porto, Portugal; DC-186 <- I. Vaz-Moreira et al.
344692007, CCUG
118962CIP <- 2007, CCUG

doi: 10.13145/bacdive14138.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Olivibacter
  • species: Olivibacter domesticus
  • full scientific name: Olivibacter domesticus (Vaz-Moreira et al. 2007) Siddiqi et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Pseudosphingobacterium domesticum

@ref: 7678

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Olivibacter

species: Olivibacter domesticus

full scientific name: Olivibacter domesticus (Vaz-Moreira et al. 2007) Siddiqi et al. 2018

strain designation: DC-186

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32090negative1.35 µm0.55 µmrod-shapedno
69480negative99.997
118962negativeoval-shapedno

pigmentation

  • @ref: 32090
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7678PLATE COUNT AGAR (DSMZ Medium 464)yeshttps://mediadive.dsmz.de/medium/464Name: PLATE COUNT AGAR (DSMZ Medium 464) Composition: Agar 15.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Dextrose 1.0 g/l Distilled water
34469MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118962CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7678positivegrowth37mesophilic
32090positivegrowth15-36
32090positiveoptimum25.5mesophilic
34469positivegrowth30mesophilic
60144positivegrowth30-37mesophilic

culture pH

@refabilitytypepH
32090positivegrowth5.5-8
32090positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32090aerobe
60144aerobe
118962obligate aerobe

spore formation

@refspore formationconfidence
32090no
69481no100
69480no99.94

halophily

@refsaltgrowthtested relationconcentration
32090NaClpositivegrowth0-5 %
32090NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3209022599arabinose+carbon source
3209017057cellobiose+carbon source
3209028757fructose+carbon source
3209028260galactose+carbon source
3209017234glucose+carbon source
3209017716lactose+carbon source
3209017306maltose+carbon source
3209037684mannose+carbon source
3209028053melibiose+carbon source
32090506227N-acetylglucosamine+carbon source
3209016634raffinose+carbon source
3209017992sucrose+carbon source
3209027082trehalose+carbon source
3209018222xylose+carbon source
320904853esculin+hydrolysis
3209017632nitrate+reduction
11896217632nitrate+reduction
11896216301nitrite-reduction

metabolite production

  • @ref: 118962
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32090catalase+1.11.1.6
32090cytochrome oxidase+1.9.3.1
118962oxidase+
118962catalase+1.11.1.6
118962urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118962-++--++-+-++++-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7678home-made compostPortoPortugalPRTEurope
60144Compost,home-madePorto ?PortugalPRTEurope2005
118962Environment, Home-made compost

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76781Risk group (German classification)
1189621Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7678
  • description: Pseudosphingobacterium domesticum 16S rRNA gene, type strain DC-186
  • accession: AM407725
  • length: 1481
  • database: ena
  • NCBI tax ID: 407022

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Olivibacter domesticus DSM 18733GCA_900109575scaffoldncbi407022
66792Pseudosphingobacterium domesticum strain DSM 18733407022.6wgspatric407022
66792Pseudosphingobacterium domesticum DSM 187332599185177draftimg407022

GC content

@refGC-contentmethod
767842.0
3209042
767838.9sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno89.21no
motileno90.397no
flagellatedno97.093yes
gram-positiveno97.58yes
anaerobicno99.153yes
aerobicyes84.665yes
halophileno92.7no
spore-formingno94.547yes
thermophileno99.14no
glucose-utilyes91.334yes

External links

@ref: 7678

culture collection no.: DSM 18733, CCUG 54353, LMG 23837, CIP 109620

straininfo link

  • @ref: 83303
  • straininfo: 292883

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625189Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost.Vaz-Moreira I, Nobre MF, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.64950-02007Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Base Composition, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Esculin/metabolism, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidoreductases/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil, *Soil Microbiology, Temperature, beta-Galactosidase/analysisEnzymology
Phylogeny22707536Olivibacter jilunii sp. nov., isolated from DDT-contaminated soil.Chen K, Tang SK, Wang GL, Nie GX, Li QF, Zhang JD, Li WJ, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.042416-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, *DDT, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny29944109Olivibacter ginsenosidimutans sp nov., with ginsenoside converting activity isolated from compost, and reclassification of Pseudosphingobacterium domesticum as Olivibacter domesticus comb. nov.Siddiqi MZ, Liu Q, Lee SY, Choi KD, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0028192018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Composting, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginsenosides/metabolism, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7678Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18733)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18733
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32090Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2833628776041
34469Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7384
60144Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54353)https://www.ccug.se/strain?id=54353
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83303Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292883.1StrainInfo: A central database for resolving microbial strain identifiers
118962Curators of the CIPCollection of Institut Pasteur (CIP 109620)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109620